QuickBooks for Windows sync setup guide

This guide will walk through setting up the sync with QuickBooks for Windows.

Tip: Back up your QuickBooks company file before proceeding.

Table of Contents

Pre setup requirements

  • Ensure anyone with shared access to the QuickBooks file to be synced is logged out
  • QuickBooks needs to be in single-user mode
    • Click File, if Switch to Multi-user Mode is available, the file is already in single-user mode.
  • Exit QuickBooks
  • QuickBooks Admin login credentials - this is required to connect the sync
  • PayMaker user in Administrator, Accountant or custom role with Sync permission
  • Administrator rights to install programs to computer or server

Install sync dashboard

The sync dashboard needs to be downloaded and installed in the same location/drive as the QuickBooks program in order to facilitate the sync between PayMaker and QuickBooks for Windows.

The QuickBooks company file does not need to be located in the same location in order to sync.


  • The sync dashboard requires Microsoft .NET framework 4.6 be enabled to run properly. If on .NET framework 4.7 or later, 4.6 may still need to be manually enabled.
  • The sync dashboard has been verified to be compatible with QuickBooks desktop 2014 and later, but may still work with older versions.

QuickBooks program installed on local computer

  1. Download the Bill.com Sync Dashboard (~955 KB)
  2. Double click the .exe file
  3. Click Next
    Run 1st page
  4. Select the drive that the QuickBooks program is installed on
  5. Click Install
  6. Click Next to confirm installation completion
    Installation complete
    • A shortcut will be created on your desktop
      Sync dashboard icon

QuickBooks program installed on Server or Hosted Server

Instructions on the installation of the sync dashboard will need to be provided to your I.T. administrator or hosting provider administrator so that the sync dashboard can be installed on your behalf.

Connect the Sync

  1. Open the Bill.com sync dashboard from the shortcut added to the desktop

  2. Open QuickBooks and log in to the company file as Admin and in single user mode

  3. In the profile editor box, click Next
    Sync dashboard and profile editor

  4. Sync dashboard will auto detect the file path of the QuickBooks company file that is open, click Next file path auto detected

  5. In QuickBooks, on the Application Certificate, select Yes, always; allow access even if QuickBooks isn't running

    • If there are multiple users on the company file, next to Login as: select Admin QB certificate
  6. Click Continue

  7. Click Done to confirm access
    Access confirmation

  8. Enter Bill.com login credentials or sync token

    • If using a Bill.com powered solution through a bank/financial institution, the sync token will be required to connect the sync
      1. In PayMaker, click the settings
      2. Click Tokens under Sync
        Tokens link
      3. Click New
        Sync token new
        • Name will auto-populate (this is a one-time use object)
          Sync token username
      4. Click Save
        • The token will be generated (also a one time use object)
          Sync token password
      5. Write down or copy & paste the username and token, before navigating away from this page, as it is only shared one time
      6. On the Sync Dashboard:
        • Email = Username
        • Password = Token
          BDC login creds
  9. Select the PayMaker Organization name to sync to
    Select org

  10. In the sync profiles box, select the profile to sync

  11. Click Sync
    Sync dashboard with profile

The sync is now connected.

Sync complete

The sync brings everything needed for payables and/or receivables from QuickBooks into PayMaker: accounts, vendors, customers, items, departments (classes), jobs (customer: jobs), and your book balance.

The first sync might take a while, depending on the size of the QuickBooks company file. Future syncs will be much faster, and QuickBooks company file will not need to be open.

PayMaker sync preferences

After the first sync completes, fill out sync preferences. Some fields will be pre-filled, review to ensure the corrects accounts have been selected.

  1. In the One last thing box, click Ok
    One last thing
  2. On the sync preferences page, select the QuickBooks accounts to use (we filled the list with your QuickBooks Chart of Accounts during the first sync) for the following settings:
    • Accounts Payable
    • Unallocated Expenses
    • Default bank account in accounting software
    • GL accounts for any bank accounts already added to PayMaker
  3. Click Save Sync preferences The sync setup is now complete.

Accounting preferences

To set additional preferences for reporting and tracking:

  1. Click Settings
  2. Under Accounting, click Preferences
  3. Click Edit
  4. Set preferences
    • Classes in QuickBooks are called Departments in PayMaker
    • Locations do not sync with QuickBooks for Windows
  5. Click Save

If you do not see the described feature available in PayMaker, you may not have access to the feature based on permissions for your role and/or your plan does not have this feature. If you wish to get access to the feature, please review the available plans for PayMaker and upgrade accordingly or contact the Administrator of your PayMaker account. Changes in monthly user fees may apply.